Equine Fecal Microbiota: What's Normal, and What's the Colitis Link?

​Colitis is a serious disease in horses that causes gastrointestinal (GI) upset, diarrhea (sometimes chronic), and even death. As researchers have learned more about the GI microbiome in humans, horses, and other species, they’ve discovered a relationship between colitis and microbiome imbalance. But does the disease cause imbalance, or does imbalance cause the disease? And what does a “normal” equine fecal microbiome look like? A Texas A&M-led research team investigated by looking at fecal samples in a diverse group of horses. Carolyn Arnold, DVM, Dipl. ACVS, an associate professor at Texas A&M, presented the team’s findings at the 2019 American Association of Equine Practitioners Convention, held Dec. 7-11, in Denver.

A Better Understanding of the Microbiome

Inside the equine gut is a complex community of bacteria, viruses, and fungi that form the GI microbiome. As scientists have learned more about these microbial populations in humans and other animals, they’ve found the health of individuals to be reliant on the “bugs” living inside them.

“As veterinarians we’re all aware we share our lives with bacteria,” said Arnold. “We are, in fact, colonized and outnumbered by them.”

Scientists once relied solely on cultures to identify bacteria. Basically, swab the sample, grow it in a petri dish, and look at the results under a microscope. Today, advances in DNA sequencing have helped them more specifically understand and identify distinct bacterial populations in different parts of the microbiota (e.g., the GI tract, reproductive tract, skin, respiratory system), Arnold said.

Dysbiosis (literally the opposite of “symbiosis”) is an imbalance of those microbes.

“What we don’t know is: Does GI disease cause dysbiosis, or does dysbiosis cause GI disease,” Arnold said. “But there’s certainly been a close relationship shown between the two.”

Research has shown that some changes in equine microbiota are caused by what Arnold called “inherent factors”—age, breed, and sex—while others are caused by “external factors” such as transportation, anesthesia, intense exercise, season, and diet.

“What is more interesting, I think, is that we’re finding more and more that there is indeed a relationship between fecal microbiota and gastrointestinal disease,” she said. “Three things in particular have been known to change the microbiome, and those include the feeding of starch in the diet, antibiotic use, and GI disease.”

The Study: Finding “Normal”

While Arnold noted the importance of previous research to describe the normal equine microbiome, she also described those studies’ limitations, which have led to variable results and no real consensus on what microbes a typical, “healthy” equine microbiome includes. She attributed those results to small sample sizes, drawing from herds in hospital settings, seasonality, and sample handling. In response,

Arnold and her co-researchers sought to characterize the microbiome in a large and diverse population of horses and compare it to horses with GI disease.

Arnold’s team used DNA sequencing to more specifically investigate fecal samples and describe microbiomes in horses from three groups:

  1. Healthy horses (80 total) not in a hospital environment or treated with non-steroidal anti-inflammatory or antibiotic drugs. They came from 15 states and included recreational, sport, and racehorses. All had known diets, and the researchers collected additional metadata, such as age, sex, location, and season, when taking samples. Additionally, the researchers recorded the amount of dietary fiber the horses received, if horses were on pasture and/or hay, and what kind (cold, transitional, or warm weather grasses). The researchers further segmented the healthy horses into five groups based on diet, ranging from those on low-starch, high-forage diets to horses receiving higher-starch concentrate diets (specifically, racehorses with large calorie needs).
  2.  Fourteen horses with colitis that had no known disease prior to antibiotic administration (AAD); and
  3.  Twelve horses with colitis from Salmonella.

Results showed that, compared to the healthy horses, those with colitis had decreased microbiome diversity.

“Decreased diversity means fewer number of bacterial species,” said Arnold. “This is important because states of health are associated with higher diversity, whereas dysbiosis is associated with decreased diversity or fewer number of species. This holds true for people and companion animals, as well.”

The researchers also found colitis to be associated dysbiosis and that AAD had a more profound limiting effect on microbiome diversity than Salmonella, Arnold said.

Additionally, the researchers did not find significant differences in horses’ microbiomes when separating them by metadata (age, sex, breed, geography, etc.). However, “by and large, diet is our main contributing factor” to microbiome differences between healthy horses, she said.

“I feel a little bit better having a diverse population of ‘healthy normals,’” Arnold said.